HsaINT0037912 @ hg19
Intron Retention
Gene
ENSG00000060718 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:2186]
Coordinates
chr1:103427422-103427821:-
Coord C1 exon
chr1:103427732-103427821
Coord A exon
chr1:103427476-103427731
Coord C2 exon
chr1:103427422-103427475
Length
256 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAA
5' ss Score
7.46
3' ss Seq
ATTTTTTTCACTTTTCCCAGGGT
3' ss Score
8.49
Exon sequences
Seq C1 exon
GGTGATCCAGGTCCTCAAGGTATCTCAGGGAAAGATGGACCAGCAGGATTACGTGGTTTCCCAGGGGAAAGAGGTCTTCCTGGAGCTCAG
Seq A exon
GTATAATCAATATCTATATAGATAAAGCAAGTGATTCCAATTGTTTATTAGAAGCATTTTTTCTCAGAACTTAAGAAGTGATGATTAAGGGAAGATATATAAACATATATATTTGATTATCATTACATATATGTGTATATATGTAGTTATGTCTATAAACATTACCTGACATCCTTATTTTACTAATCAGATATCTCCTCCTATTGGTATTCAATTCATATGGATTCATTTTCTTTATTTTTTTCACTTTTCCCAG
Seq C2 exon
GGTGCACCTGGACTGAAAGGAGGGGAAGGTCCCCAGGGCCCACCAGGTCCAGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000060718-COL11A1:NM_001190709:39
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(15.2=40.0),PF0139113=Collagen=FE(39.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.3=100),PF0139113=Collagen=PU(19.8=94.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)